Hi Vandna,
Assuming you have two copies, chain A and B.
In UCSF chimera:
1) open two copies of the pdb (model #0 and #1)
2) in command line, type:
match #1:.B@CA #0:.A@CA showMatrix true
Besides moving model #1 chain B to model #0 chain A, the match command
also outputs the rotation and translation matrices and angles, axes in
Favorite-> Reply Log.
Note that you might need to specify residue number range for the two
chains if the number of CAs in them are not equal - just to make the
match working. The match command does not guess the range of residues to
align as the MatchMaker does. Alt confs involving CAs also count. You
may run:
del @CA.B
to delete all alt conf B CA atoms before the match command to make it
working
If you wish to draw the rotation axis in Chimera, you need to make a
bild file that draws an arrow from the "Axis point" with direction
specified by the Axis vector. Assuming the "Axis" is "Ax Ay Az" and the
"Axis point" is "x y z", you need to calculate X1=x+Ax*20, Y1=y+Ay*20,
Z1=z+Az*20, then put this in the arrow.bld file:
.arrow x y z X1 Y1 Z1
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html
COOT also outputs the matrices in the terminal window. But COOT does not
seem to directly show the more human friendly "rotation angle" and
"shift along axis".
Zhijie
On 29/06/2017 3:16 PM, Vands wrote:
Hi every one ,
I am looking for a tool to perfectly determine
the NCS axis. I have two forms of crystals where diamer is with NCS
but on a comparison of both forms, it looks like NCS axis is little
off when i superpose two forms, i would like to measure rotation or
translation between axes .
--
Vandna Kukshal
Senior Scientist
Dept. Biochemistry and Molecular Biophysics
Washington University School of Medicine
660 S. Euclid, Campus Box 8231
St. Louis, MO 63110
